Saturday, 28 March 2015

There and Back Again...and again

Dinosaur Gallery, MfN, featuring Giraffatitan,
Apatosaurus, Dicraeosaurus and Archaeopteryx
One of the many benefits of studying animal osteology is that I get to travel to some pretty awesome places. Okay, so not fieldwork in the Bahamas or South Africa, like some of my colleagues in the lab, but museums can be awesome too! One of the largest collections in western Europe can be found at the world famous  Museum für Naturkunde (MfN) in Berlin, Germany. The MfN houses, among other things, the tallest mounted skeleton in the world - a Giraffatitan brancai - along with the famous 'Berlin Specimen' of the ancient bird Archaeopteryx. Less well known are the extensive mammalian, avian and alcohol-preserved collections. For my part, the fossil and extant mammal collections house a broad range of material from both living and extinct perissodactyls.

For my first visit to the collections I was accompanied by my girlfriend and on-the-day assistant Eleni, who made my job of finding and identifying which spevimens were good to use SOOO much easier! Our supervisor for the extant equids and tapirs collection was Mrs. Christiane Funk - collections manager for mammals at the MfN. With the combined forces of the three of us, we managed to log all the tapir and equid specimens in less than four hours...which by my standards is pretty speedy! Subsequent visits involved some pretty heavy lifting of suitcases full of bones, sweaty-nerding out in the fossil collections and several traipses through the Zoological Gardens, all of which were very enjoyable! I have also become intimately familiar with the new tram system, watched the road outside the museum take on a new shape every time I visit, and on the odd occasion lost my passport, hurling my holiday plans into turmoil! (I have a new one now, thankfully!)

My interest in the MfN collections are three-fold: first and foremost, I hope to use the described tapir specimens from the mammal collection to supplement the specimens we have already scanned from institutions in Belgium, the Netherlands, France and Austria. The acquisition of multiple specimens is essential to attain and account for as much variation in the bones as possible.
Secondly, I plan to use three unidentified tapir specimens to test whether geometric morphometrics can be used to distinguish tapir specimens at the species level. This project is in combination with colleagues at the KMDA, Antwerp, who will be testing the specimens using molecular markers from bone cores. The results of this study will hopefully enable museum collections to utilise a 'morphometric toolbox' for the positive identification of tapir specimens with no species denomination or locality information - essentially, making a useless specimen useful without invasive genetic sampling!
Comparison of Black Rhinoceros and the Giant Rhino Elasmotherium 
fischeri (based on MB.Ma. 26313). The Giant Rhino made a screen 
appearance on Nigel  Marven's Prehistoric Park on ITV (bottom right)
Lastly, we currently have a masters project looking into the morphological variation of the third metacarpal - an exemplar bone for many analyses on equids. To place this variation in a phylogenetic context, specimens from the fossil mammal collection have been loaned to us by Collections Manager Mr. Thomas Schossleitner and renowned vertebrate palaeontologist Dr. Oliver Rahut. Specimens have included equids from the Plio/Pleistocene, tridactyl hipparionine equids from the Pliocene, and a wide range of rhinoceroses ranging from the Miocene to the late Pleistocene (including the Giant Rhinoceros, Elasmotherium). To compliment these crown groups, we have also been granted specimens of brontotheres/titanotheres and the small, enigmatic palaeotheres; both these groups come from the Eocene epoch, over 40 million years ago!

Dice playing in a zebra's graveyard...
...and gazing at a long lost cousin
All in all, my yo-yo-ing to Berlin and back has been very fulfilling. Aside from learning how painful Eurolines coaches can be, I have had the opportunity to visit behind the scenes of one of the greatest museums of natural history in Europe, possibly the world. I would like to extend my thanks to all the staff at the Museum für Naturkunde, especially Christiane and Thomas, for their patient hospitality and for allowing me access to specimens that will prove invaluable to the continuation of my project. I always enjoy visiting, and I look forward to doing so again in the near future. 

Thanks to all for reading - stay tuned for my next research adventure! Ciao for now and guten tag!

Thursday, 12 March 2015

A GMM Phylogeny of Wine - ants, plants and biology bants in Pierola, Barcelona

So, quick spoiler, I wrote this a while back, so apologies for the peculiar structure of the report - I hope you still like it!

So I find myself once more in the somewhat familiar surroundings of Zaventam airport, Brussels. Destination: Barcelona - 3rd time in under a year, lucky sod that I am! This time I do not travel alone - as Batman had Robin, Laurel had Hardy, and George W Bush had a decorative pot plant, my informative and plucky young sidekick for this tour to El Hostalets de Pierola in the absence of Zebo was Masters student Hester Hanegraef. Hester will be studying in the same lab on the same material as I, in a slightly less rigorous nature, and so this was a perfect opportunity for her and I to learn more about the techniques we can use on our specimens to test evolutionary hypotheses and, more importantly, paella-eating ability. We were joined in secret by my new mini-mascot, Dice. He will crop up throughout my PhD, so keep an eye out!

The course is organised by Dr. Sole Estaban as part of Transmitting Science, a company that has been established to provide detailed scientific experience and expertise in a wide variety of fields ranging from fundamentals of biomechanics to illustrative drawing. This was my second course, and focused on the use of Geometric Morphometrics in Phylogeny ('family tree') and the various ways that phylogenetic methods could be implemented to extract biological meaning from shape data. The course was run by Prof. Chris Klingenburg (University of Manchester), a renowned name in the field of morphometrics, whose intuitive knowledge of the program MorphoJ would be invaluable to us lesser mortals as we struggle with making sense of our data. Mind you, he should know all about it, he wrote the program...
School time at Pierola. Prof. Chris Klingenburg walking us through the processes with MorphoJ. Mini-mascot Dice the Diceros watches on as I manipulate a rhinoceros scapula on Landmark Editor. 

Overall, I must say that the course was a resounding success. With a low attendance (n=9) this gave everyone a great opportunity to interact with all other participants during the workshop, and with Chris whenever anything went drastically wrong! With attendees from Brazil, USA,  UK, South Africa and Northern Europe, this course was a testament to the success of the Transmitting Science franchise. It must be said that I wrote a lot down without necessarily always understanding every bit of it, but the knowledge I gained from the analyses I ran has set me up with brand new ideas for where my project can go. So if anyone has a repository of fossil horse feet they fancy lending me for purely scientific purposes, that would be swell!

As always, the academic and extra-curricular activities are equally as important during a course such as this. Aside from a wealth of morphometric and phylogenetic knowledge, this week we discovered:
1. When you have the worlds largest repository of leaves for an endemic group of plants, morphometrics is the way to keep masters students busy...
2. Music is wine, barriers are burritos, p-values mean nothing and everything, weasels are dimorphic, the "secret stash" is basically in the kitchen, icecream is a sandwich, PhD students look at pictures not numbers, gravity always wins, and at the end of the day garlic makes everything better...
3. Fleas bite you in straight lines. Mosquitos dont give a s**t. Ants LOVE aioli, and favour apple and butifarra in equal measure (suggesting that, with 95% certainty and a p-value of <0.05, the ants are from Catalonia)...
4. Vegetarianism is rife, as long as the parameters for being a vegetarian include: "will eat fish"...
Fantastic vineyard visit on the way back to Barcelona at the end of the course. Beautiful weather and top quality grape-juice!

It must be said I had another really rewarding experience in Barcelona, coupled with some delightful wine-tasting in the Catalan hills, and look forward to returning some day soon. My thanks extend to Chris, Sole and all the Transmitting Science staff, and special thanks to the Catalan people for making us so welcome.

Tuesday, 9 September 2014

FWO Success! A new direction for the project


Last June I learned that my application for a 4 year project specialising in morphometrics and osteology of the forelimb of Perissodactyla (horses and their relatives) was approved, and I therefore "began" my PhD afresh in October...2014...yes, ok, I have been sitting on this one for a while!

Obviously, this is not entirely accurate - I have not in fact "started again", as I have already begun my PhD sponsored by the grant awarded to my supervisor Dr. Sandra Nauwelaerts. This project is looking at gait analysis in perissodactlys, recently working on Grevy's Zebra, Malayan and Lowland tapirs. From October 2014, I began taking the project in a brand new direction, which is very exciting. With additional funding for an extra year, this has offered me a great opportunity to get the very best out of the project, and test some very interesting biological questions regarding perissodactyl locomotor mechanics and morphological evolution.

My FWO (Fonds voor Wetenschappelijk Onderzoek) grant allows me to pursue an osteological and morphometric avenue of research. This new funding is enabling me to focus my energies on collecting museum samples for scanning, and analysing the scanned material using 3D landmark analyses, testing for integration and phylogenetic/ecological signal. 

The sub-project I am now working on will look to assess the morphological variation within the forelimbs of extant tapirs. For those who are not aware, tapirs are primitive, long-nosed, pig-like relatives of rhinos and horses! There are five extant species: The large Malayan tapir; the Central American Baird's Tapir; the relatively well known Lowland Tapir; the small, woolly Mountain Tapir; and the recently described Kabomani, or Little Black Tapir (link to Scientific American article: Tetrapod Zoology: new-living-species-of-tapir.)
Currently, I am assessing the morhological differences within the forelimb skeleton of modern tapirs, looking to find morphological differences using 3D morphometrics to show up variation not previously described. This way, we hope to result in a morphometric 'tool-box' for assessing museum specimens of tapirs without invasive sampling! So far we have fully scanned sixteen specimens, with plenty more to come. Here is a chance for me to thank the museums from Berlin (Museum fur Naturkunde), Vienna (Naturhistoriches Museum Wien), Paris (Museum National d'Histoire Naturelle) and Leiden (Naturalis Biodiversity Centre), in addition to Mr. Luc Tyteca, a private collector who has provided invaluable support to the project so far! To give you a sense of the scans we have taken, here is a rendering of a limb from a Baird's tapir I recently processed in Blender:

Render of RMMNH 43495 Tapirus bairdii, courtesy of the Naturalis Biodiversity Centre, Leiden, NL

Ciao for now readers - I very much appreciate your time if you bothered to read this far! Next blog will be a review of my excursion to Barcelona in September!

Until then, goedenavond and good night :)

Tuesday, 27 May 2014

Zebo's Adventures - Geometric Morphometrics in Barcelona

So, the epic voyage begins. Striding out into a brand new world (well, not entirely, I'll explain later), Zebo and I have made it to the Transmitting Science course on Geometric Morpohometrics. The course was being held, as with many of Transmitting Science's courses and workshops, in the picturesque surroundings of the Pyreneean foothills, beneath the shadow of Montserrat, at the Centre de Restoracio i Interpretacio Palaeontologic (CRIP). Before the relatively brief, if rather sleep-inducing, voyage from Placa de Catalunya to the field centre/hostel at CRIP, Zebo decided he would like to taste some local ale at a friendly (if rather American) tapas bar. Unfortunately, Catalonian law dictates no alcohol is to be served to convicted golf club covers, how ever much they bray in protest. In light of this, we shared a Coke.

On arrival at the field centre in the mountains, 15 humans, two equids and a child converged on the labs of the CRIP - a fascinating place, most famous for the local legend Pau (Pierolapithicus catalunicus). We were lead by co-founder of Transmitting Science, Dr. Sole Estaban, without whom we would not have been able to attend such an informative course. The scientists at the Pierola site have discovered a wide array of fossil material, including turtles, rhinoceros, a wide variety of primates, and even the odd dinosaur! Due to the mountainous nature of the landscape, one occasionally found oneself above the clouds - not something Zebo was entirely familiar with! For more information on the centre, and the great restoration and preservation work they do there, find them at

Over the ensuing days, it can be said that a great many things were learned. On the academic side, our multi-cultural, multi-lingual group discovered the many delights of applying geometric morphometrics (method for analysis of shape, independent of size and orientation) to 3D scans in Landmark Editor - a free software package that can be used to visualise and place landmark data onto scans, such as horse bones. This software is the product of the Institute for Data Analysis and Visualisation at the University of California, and is being used dramatically increase the options biologists, palaeontologists and even mineralogists have at their disposal for assessing shape data in three dimensions. More info on the program can be found at
Throughout the course, we also dabbled in Morphologika, MorphoJ, PAST (which since its renovations has become rather odd!), Meshlab, Checkpoint - the list goes on. It can safely be said that much knowledge was gleaned from our excellent instructor, the effervescent Dr. Melissa Tallman, and that no matter what organisms we are planning to study, we will now know how to apply the programs to answer our question...well, for the most part!

It must be said that these computationally intensive skills were not the only things learnt on this excursion - the conveniently located bar not 30 seconds walk from the classroom provided the setting for a diverse range of discussion topics. Subjects included (but were not limited to):
1) the orientation of the swastica, and how it would be so much easier if the Nazis had taken the mean average shape of the symbol so as not to confuse dyslexic graduate students in the 2010s (points clockwise, for those still unsure);
2) the incontrovertible fact that a yard of ale is nothing more or less than three feet in height;
3) the reenactment of 18th Century naval battles by hermaphroditic sea slugs, firing sperm at one another a'broadside, presumably in order to minimise foreplay and get on in life;
4) various and nefarious regional songs, including Dominick the Italian Christmas Donkey, which lead us on a greasy slope, past Nelly the Elephant, to the subject of Christmas. Frankly, I must say that a quail inside a chicken inside a duck inside a turkey inside a goose inside a swan is an inspired idea for Christmas dinner...but Turducken will suffice for the moment;
5) and finally, the apparent confusion and utter division of opinion as to whether one should or should not apply phylogenetic corrections to ones data, resulting in a 2hr debate with no tangible outcome!
At one point, Zebo became so frustrated with the utter futility of one conversation (something about a siege and a carrier pigeon...) that he was driven to fags and booze:

All in all, the course was a roaring success in my eyes, and I hope for the rest of the participants also. Both Zebo and I would like to thank Sole, Lissa and the fine people at the hostel for their organisation, their patience, their culinary expertise respectively...and, of course, their coffee. It has been a memorable trip, I have made many good contacts and hopefully some good friends, all of whom I hope to see on the academic circuit in the near future.

That's all folks. Until the next instalment of Zebo's Adventures, it's goodbye from me, and its *neigh-neigh* from him.